Summary

Target folder: /home/hflavio/Google-drive/workshops_and_presentations/2024-09_OTN/workshop_materials/dataset/2017

Timestamp: 2024-07-24 12:49:21.706166

Number of target tags: 99

Number of listed receivers: 13 (of which 0 had no detections)

Data time range: 2017-04-12 09:20:23 to 2017-06-13 04:37:34 (Europe/London).

Percentage of post-release valid detections: 19.23%

Found a bug? Report it here.

Want to cite actel in a publication? Run citation('actel')

Study area

Arrays with the same background belong to the same section. Release sites are marked with “R.S.”. Arrays connected with an arrow indicate that the animals can only pass in one direction.

Receiver stations

Station.name Latitude Longitude Array Section Standard.name x.29902 y.29902
Bellisle 55.1095 -6.44540 A1 River St.1 299262 430242
Bush Hydro Int. 55.1963 -6.52610 A2 River St.2 293908 439793
Leap Upstream 55.1967 -6.52615 A2 River St.3 293904 439837
smolt layde 55.2014 -6.52430 A3 River St.4 294010 440363
S. works Rep 55.2104 -6.53170 A4 River St.5 293518 441355
Golf Course 55.2196 -6.53190 A5 River St.6 293484 442379
Runkerry bay 1 55.2216 -6.54160 A6 Sea St.7 292862 442588
Runkerry bay 2 55.2243 -6.54180 A6 Sea St.8 292843 442889
Runkerry bay 3 55.2263 -6.53890 A6 Sea St.9 293023 443115
Runkerry bay 4 55.2280 -6.53610 A6 Sea St.10 293197 443308
Outer bay 1 55.2234 -6.55560 A7 Sea St.11 291967 442770
Outer bay 2 55.2261 -6.55740 A7 Sea St.12 291846 443068
Outer bay 3 55.2285 -6.55530 A7 Sea St.13 291974 443338

Deployments

Receiver Array Station.name Standard.name Start Stop
102881 A4 S. works Rep St.5 2017-01-01 00:00:01 2018-01-01 00:00:01
102883 A2 Bush Hydro Int. St.2 2017-01-01 00:00:01 2018-01-01 00:00:01
107157 A6 Runkerry bay 4 St.10 2017-01-01 00:00:01 2018-01-01 00:00:01
108999 A6 Runkerry bay 3 St.9 2017-01-01 00:00:01 2018-01-01 00:00:01
109004 A6 Runkerry bay 2 St.8 2017-01-01 00:00:01 2018-01-01 00:00:01
111468 A2 Leap Upstream St.3 2017-01-01 00:00:01 2018-01-01 00:00:01
126671 A1 Bellisle St.1 2017-01-01 00:00:01 2018-01-01 00:00:01
128987 A3 smolt layde St.4 2017-01-01 00:00:01 2018-01-01 00:00:01
128988 A5 Golf Course St.6 2017-01-01 00:00:01 2018-01-01 00:00:01
128992 A6 Runkerry bay 1 St.7 2017-01-01 00:00:01 2018-01-01 00:00:01
546169 A7 Outer bay 2 St.12 2017-01-01 00:00:01 2018-01-01 00:00:01
546170 A7 Outer bay 1 St.11 2017-01-01 00:00:01 2018-01-01 00:00:01
546646 A7 Outer bay 3 St.13 2017-01-01 00:00:01 2018-01-01 00:00:01

Release sites

Station.name Latitude Longitude Array Type Standard.name x.29902 y.29902 n.Wild
Cross 55.10060 -6.4053 A1 Release Cross 301843 429309 30
Trap 55.20271 -6.5231 A4 Release Trap 294084 440510 69

Array forward efficiency

Note:
These efficiency calculations do not account for backwards movements. This implies that the total number of animals to have been last seen at a given array may be lower than the displayed below. Please refer to the section survival overview and last seen arrays to find out how many animals were considered to have disappeared per section.
The data used in the tables below is stored in the overall.CJS object. Auxiliary information can also be found in the matrices and arrays objects.
These efficiency values are estimated using the analytical equations provided in the paper “Using mark-recapture models to estimate survival from telemetry data” by Perry et al. (2012). In some situations, more advanced efficiency estimation methods may be required.
You can try running advEfficiency(results$overall.CJS) to obtain beta-drawn efficiency distributions (replace results with the name of the object where you saved the analysis).

Individuals detected and estimated

A1 A2 A3 A4 A5 A6 A7
detected 24 16 16 8 50 37 19
here plus on peers 16 16 14 8 38 17 -
not here but on peers 0 0 0 43 1 2 -
known 24 16 16 51 51 39 19
estimated 24 16 16 51 51 41 -

Array efficiency

Note: These values already include any intra-array efficiency estimates that have been requested.

A1 A2 A3 A4 A5 A6 A7
efficiency 100% 100% 100% 15.7% 97.4% 89.5% -

Warning messages

Warning: 'speed.warning'/'speed.error' were not set, skipping speed checks.
Warning: Tag R64K-2764 (5/64) was detected 233 times at stations less than 1.5 km apart in array 'A4' (St.5), over 26.51 days and then disappeared. Could it be inactive?
Warning: Tag R64K-2776 (13/64) was detected 47608 times at stations less than 1.5 km apart in array 'A6' (St.7, St.8), over 40.32 days and then disappeared. Could it be inactive?
Warning: Tag R64K-2791 (21/64) jumped through 5 arrays from release to first valid event (Release -> A6).
Warning: Tag R64K-2791 (21/64) jumped through 4 arrays in valid events 1 -> 2 (A6 -> A1).
Warning: Tag R64K-2791 (21/64) jumped through 2 arrays in valid events 4 -> 5 (A3 -> A6).
Warning: Tag R64K-2791 (21/64) was detected 4 times at stations less than 1.5 km apart in array 'A6' (St.7), over 11.57 days and then disappeared. Could it be inactive?
Warning: Tag R64K-2792 (22/64) jumped through 4 arrays from release to first valid event (Release -> A5).
Warning: Tag R64K-2792 (22/64) jumped through 3 arrays in valid events 1 -> 2 (A5 -> A1).
Warning: Tag R64K-2811 (38/64) was detected 11746 times at stations less than 1.5 km apart in array 'A4' (St.5), over 27.77 days and then disappeared. Could it be inactive?
Warning: Tag R64K-2851 (60/64) has less than 2 detections in total. Discarding this tag.
Warning: Inter-section backwards movements were detected for tag R64K-2849 (58/64) and the last events are not ordered!

User comments

No comments were included during the analysis.

Biometric graphics

Note:
The data used in this graphic is the data present in the biometrics.csv file.

Section Survival

Note:
The data used in this table and graphic is stored in the section.overview object.
Total Disap..in.River Migrated.to.Sea Disap..in.Sea Succeeded
Wild 99 48 51 12 39

Last Seen Arrays

Note:
The data used in this graphic is stored in the status.df object (‘Very.last.array’ column).

Progression

Zoom in or open the figure in a new tab to clearly read the text within each circle.

Note:
The progression calculations do not account for backwards movements. This implies that the total number of animals to have been last seen at a given array may be lower than the displayed below. Please refer to the section survival overview and last seen arrays to find out how many animals were considered to have disappeared per section.
The data used in this graphic is stored in the overall.CJS object, and the data used in the tables is stored in the group.overview object. You can find detailed progressions per release site in the release.overview object.

Group: Wild

Release A1 A2 A3 A4 A5 A6 A7
detected 99 24 16 16 8 50 37 19
here plus on peers - 16 16 14 8 38 17 -
not here but on peers - 0 0 0 43 1 2 -
known 99 24 16 16 51 51 39 19
estimated - 24 16 16 51 51 41 -
difference - 0 0 0 0 0 2 -

Time of arrival at each Array

Note:
Coloured lines on the outer circle indicate the mean value for each group and the respective ranges show the standard error of the mean. Each group’s bars sum to 100%. The number of data points in each group is presented between brackets in the legend of each pannel.
You can replicate these graphics and edit them as needed using the plotTimes() function.
The data used in these graphics is stored in the times object.
To obtain reports with the legacy linear circular scale, run options(actel.circular.scale = "linear") before running your analyses.
/tmp/Rtmpe00LlA/actel_report_auxiliary_files/circular_svg_print_failure_bounce_back.png /tmp/Rtmpe00LlA/actel_report_auxiliary_files/circular_svg_print_failure_bounce_back.png /tmp/Rtmpe00LlA/actel_report_auxiliary_files/circular_svg_print_failure_bounce_back.png /tmp/Rtmpe00LlA/actel_report_auxiliary_files/circular_svg_print_failure_bounce_back.png

Dotplots

Note:
The top 10% of the values for each panel are marked in red.
The bottom 10% of the values for each panel are marked in blue.
The columns starting with “To” should be read as either “Average time to …” or “Average speed to …”, depending on the unit used. The columns starting with “In” should be read as “Total time in …”. These reductions were made to keep the column headers as short as possible.
The data used in these graphics is stored in the status.df object.

Individual detection plots

Note:
You can choose to plot detections by station or by array using the detections.y.axis argument.
The detections are coloured by section. The vertical black dashed line shows the time of release. The vertical grey dashed lines show the assigned moments of entry and exit for each study area section. The full dark-grey line shows the movement events considered valid, while the dashed dark-grey line shows the movement events considered invalid.
Manually edited tag detections are highlighted with yellow graphic borders.
Manually overridden tag detections are highlighted with red graphic borders.
The arrays have been aligned by section, following the order provided either in the spatial input or the section.order argument.
You can replicate these graphics and edit them as needed using the plotDetections() function.
You can also see the movement events of multiple tags simultaneously using the plotMoves() function.
The data used in these graphics is stored in the detections and movements objects (and respective valid counterparts).

Full log

Actel R package report.
Version: 1.3.0.9007

Target folder: /home/hflavio/Google-drive/workshops_and_presentations/2024-09_OTN/workshop_materials/dataset/2017
Timestamp: 2024-07-24 12:49:21.706166
Function: migration()

M: 'report' option has been activated.
M: Importing data. This process may take a while.
M: No Code.space column was found in the biometrics. Assigning code spaces based on detections.
M: Number of target tags: 99.
M: Matching detections with deployment periods.
M: Number of ALS: 13 (of which 0 had no detections)
M: Data time range: 2017-04-12 09:20:23 to 2017-06-13 04:37:34 (Europe/London).
M: File 'distances.csv' found, activating speed calculations.
M: Data successfully imported!
M: Creating movement records for the valid tags.
M: Checking movement events quality.
Warning: 'speed.warning'/'speed.error' were not set, skipping speed checks.
Warning: Tag R64K-2764 (5/64) was detected 233 times at stations less than 1.5 km apart in array 'A4' (St.5), over 26.51 days and then disappeared. Could it be inactive?
M: ALL movement events from tag R64K-2764 were rendered invalid per user command.
Warning: Tag R64K-2776 (13/64) was detected 47608 times at stations less than 1.5 km apart in array 'A6' (St.7, St.8), over 40.32 days and then disappeared. Could it be inactive?
M: 15 movement event(s) from tag R64K-2776 were rendered invalid per user command.
Warning: Tag R64K-2791 (21/64) jumped through 5 arrays from release to first valid event (Release -> A6).
Warning: Tag R64K-2791 (21/64) jumped through 4 arrays in valid events 1 -> 2 (A6 -> A1).
Warning: Tag R64K-2791 (21/64) jumped through 2 arrays in valid events 4 -> 5 (A3 -> A6).
M: Movement event(s) 1 from tag R64K-2791 were rendered invalid per user command.
Warning: Tag R64K-2791 (21/64) was detected 4 times at stations less than 1.5 km apart in array 'A6' (St.7), over 11.57 days and then disappeared. Could it be inactive?
Warning: Tag R64K-2792 (22/64) jumped through 4 arrays from release to first valid event (Release -> A5).
Warning: Tag R64K-2792 (22/64) jumped through 3 arrays in valid events 1 -> 2 (A5 -> A1).
M: Movement event(s) 1 from tag R64K-2792 were rendered invalid per user command.
Warning: Tag R64K-2811 (38/64) was detected 11746 times at stations less than 1.5 km apart in array 'A4' (St.5), over 27.77 days and then disappeared. Could it be inactive?
M: ALL movement events from tag R64K-2811 were rendered invalid per user command.
Warning: Tag R64K-2851 (60/64) has less than 2 detections in total. Discarding this tag.
M: Compiling and checking section movements for the valid tags.
Warning: Inter-section backwards movements were detected for tag R64K-2849 (58/64) and the last events are not ordered!
M: Movement event(s) 3 from tag R64K-2849 were rendered invalid per user command.
M: Rendering 1 array movement(s) invalid for tag R64K-2849 as the respective section movements were discarded by the user.
M: Filtering valid array movements.
M: Filtering valid section movements.
M: Compiling migration timetable.
M: Compiling summary information tables.
M: Calculating array efficiency.
M: Saving results as 'actel_migration_results.RData'.
M: Producing the report.
M: Drawing individual detection graphics.
M: Analysis completed!

-------------------
User interventions:
-------------------
y # save strays?
y # invalidate/expand moves in R64K-2764?
1:23
y # confirm?
y # invalidate/expand moves in R64K-2776?
3:17
y # confirm?
n # invalidate more?
y # invalidate/expand moves in R64K-2791?
1
y # confirm?
n # invalidate more?
n # invalidate/expand moves in R64K-2791?
y # invalidate/expand moves in R64K-2792?
1
y # confirm?
n # invalidate more?
y # invalidate/expand moves in R64K-2811?
1:69
y # confirm?
y # invalidate/expand moves in R64K-2849?
3
y # confirm?
n # invalidate more?
y # save results?
-------------------
Migration function call:
-------------------
migration(tz = 'Europe/London', section.order = NULL, datapack = NULL, success.arrays = c('A6', 'A7'), max.interval = 60, min.total.detections = 2, min.per.event = c(1, 1), start.time = NULL, stop.time = NULL, speed.method = 'last to first', speed.warning = NULL, speed.error = NULL, jump.warning = 2, jump.error = 3, inactive.warning = 5, inactive.error = 5, exclude.tags = NULL, override = NULL, report = TRUE, auto.open = TRUE, discard.orphans = FALSE, discard.first = NULL, save.detections = FALSE, if.last.skip.section = TRUE, replicates = NULL, disregard.parallels = TRUE, GUI = 'needed', save.tables.locally = FALSE, print.releases = TRUE, detections.y.axis = 'auto')
-------------------

Index:

Summary Study area Stations Deployments Release sites Array efficiency Warnings Comments Biometrics Section survival Last seen Progression Arrival times Dotplots Individual detections Full log